.TH gmx-convert-tpr 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file

.SH SYNOPSIS
gmx convert-tpr [\-s [<.tpr/.tpb/...>]] [\-f [<.trr/.cpt/...>]]
             [\-e [<.edr>]] [\-n [<.ndx>]] [\-o [<.tpr/.tpb/...>]]
             [\-nice <int>] [\-extend <real>] [\-until <real>]
             [\-nsteps <int>] [\-time <real>] [\-[no]zeroq] [\-[no]vel]
             [\-[no]cont] [\-init_fep_state <int>]

.SH DESCRIPTION
\fBgmx convert\-tpr\fR can edit run input files in four ways.

\fB1.\fR by modifying the number of steps in a run input file with options \fB\-extend\fR, \fB\-until\fR or \fB\-nsteps\fR (nsteps=\-1 means unlimited number of steps)

\fB2.\fR (OBSOLETE) by creating a run input file for a continuation run when your simulation has crashed due to e.g. a full disk, or by making a continuation run input file. This option is obsolete, since mdrun now writes and reads checkpoint files. \fBNote\fR that a frame with coordinates and velocities is needed. When pressure and/or Nose\-Hoover temperature coupling is used an energy file can be supplied to get an exact continuation of the original run.

\fB3.\fR by creating a \fB.tpx\fR file for a subset of your original tpx file, which is useful when you want to remove the solvent from your \fB.tpx\fR file, or when you want to make e.g. a pure Calpha \fB.tpx\fR file. Note that you may need to use \fB\-nsteps \-1\fR (or similar) to get this to work. \fBWARNING: this \fB.tpx\fR file is not fully functional\fR.

\fB4.\fR by setting the charges of a specified group to zero. This is useful when doing free energy estimates using the LIE (Linear Interaction Energy) method.

.SH OPTIONS
Options to specify input and output files:

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Run input file: tpr tpb tpa

.BI "\-f" " [<.trr/.cpt/...>] (traj.trr) (Input, Optional)"
    Full precision trajectory: trr cpt trj tng

.BI "\-e" " [<.edr>] (ener.edr) (Input, Optional)"
    Energy file

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Index file

.BI "\-o" " [<.tpr/.tpb/...>] (tpxout.tpr) (Output)"
    Run input file: tpr tpb tpa


Other options:

.BI "\-nice" " <int> (0)"
    Set the nicelevel

.BI "\-extend" " <real> (0)"
    Extend runtime by this amount (ps)

.BI "\-until" " <real> (0)"
    Extend runtime until this ending time (ps)

.BI "\-nsteps" " <int> (0)"
    Change the number of steps

.BI "\-time" " <real> (-1)"
    Continue from frame at this time (ps) instead of the last frame

.BI "\-[no]zeroq" "  (no)"
    Set the charges of a group (from the index) to zero

.BI "\-[no]vel" "  (yes)"
    Require velocities from trajectory

.BI "\-[no]cont" "  (yes)"
    For exact continuation, the constraints should not be applied before the first step

.BI "\-init_fep_state" " <int> (0)"
    fep state to initialize from


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.